7W36 | pdb_00007w36

Crystal structure of human Atg5 complexed with a stapled peptide

• PDB DOI: https://doi.org/10.2210/pdb7W36/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-11-25 Released: 2022-09-21 
• Deposition Author(s): Kurata, I., Matoba, K., Noda, N.N.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.287 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.245 (Depositor) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Targeting the ATG5-ATG16L1 Protein-Protein Interaction with a Hydrocarbon-Stapled Peptide Derived from ATG16L1 for Autophagy Inhibition.

Cui, J., Ogasawara, Y., Kurata, I., Matoba, K., Fujioka, Y., Noda, N.N., Shibasaki, M., Watanabe, T.

(2022) J Am Chem Soc 144: 17671-17679

• PubMed: 36107218 
• DOI: https://doi.org/10.1021/jacs.2c07648
• Primary Citation Related Structures: 
  7W36


• PubMed Abstract: 
  

  Selective modulation of autophagy is a promising therapeutic strategy, especially for cancer treatment. However, the lack of specific autophagy inhibitors limits this strategy. The formation of the ATG12-ATG5-ATG16L1 complex is essential for targeting the ATG12-ATG5 conjugate to proper membranes and to generate LC3-II for the progression of autophagy. Thus, targeting ATG5-ATG16L1 protein-protein interactions (PPIs) might inhibit early stage autophagy with high specificity. In this paper, we report that a stapled peptide derived from ATG16L1 exhibits potent binding affinity to ATG5, striking resistance to proteolysis, and significant autophagy inhibition activities in cells.

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Organizational Affiliation: 
• Institute of Microbial Chemistry (BIKAKEN), Tokyo, 3-14-23 Kamiosaki Shinagawa-ku, Tokyo, 141-0021, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 35.31 kDa 
• Atom Count: 2,352 
• Modeled Residue Count: 283 
• Deposited Residue Count: 298 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy protein 5	A	275	Homo sapiens	Mutation(s): 0  Gene Names: ATG5, APG5L, ASP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H1Y0 (Homo sapiens) Explore Q9H1Y0  Go to UniProtKB:  Q9H1Y0
PHAROS:  Q9H1Y0 GTEx:  ENSG00000057663

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Stapled ATG16L1-derived peptide	B	23	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q676U5 (Homo sapiens) Explore Q676U5  Go to UniProtKB:  Q676U5
PHAROS:  Q676U5 GTEx:  ENSG00000085978

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MK8	B	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.287 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.245 (Depositor) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.794	α = 90
b = 73.083	β = 90
c = 102.127	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-21 
Deposition Author(s): Kurata, I., Matoba, K., Noda, N.N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)		19H05707
Japan Science and Technology		JPMJCR20E3

Revision History  

• Version 1.0: 2022-09-21
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2023-11-29
  Changes: Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary